Announcements:

• Eivind Valen named NCMM Associate Investigator

Press (mostly Norwegian):

• Nye metoder for lesing av DNA gir bedre utsikter
• Discovery of Apela/Toddler
• Rekruttering til Bergen
• Kartleggingen av menneskets promotere

Interviews (mostly Norwegian):

• Forskerforum - Her er forskernes beste tips for å holde seg faglig oppdatert
• Forskning.no - Så langt har forskere kommet med å bruke gensaksen CRISPR på mennesker
• Forskning.no - Dataprogram avdekker fusk i cellene dine
• Forskningsetikk og Teknisk Ukeblad - Frykt og håp rundt ny genteknologi

Panel debates (mostly Norwegian):

• Bergen Film Festival - Alt du vil vite om CRISPR (men ikke våger å spørre om)
• Arendalsuka - KUNSTIG INTELLIGENS I HELSESEKTOREN: NØKKELEN TIL ET LENGRE LIV, MEN…?

Video:

• Study bioinformatics at UiB (Norwegian)

I teach BINF201: Introduction to Omics

Poster

• Haugen, Frida Loe; Mamia, Katariina Aino Inkeri; Rio, Oline Eriksen et al. (2025). CRISPR/Cas9-based pipeline to introduce custom edits in autologous T cells. (external link)
• Haugen, Frida Loe; Mamia, Katariina Aino Inkeri; Rio, Oline Eriksen et al. (2025). CRISPR-Cas9 pipeline for custom editing in autologous T cells. (external link)
• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)
• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)
• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)
• Mamia, Katariina Aino Inkeri; Saarela, Janna Saija; Li, Zhuokun et al. (2022). CRISPR-Cas9 T cell editing pipeline for Finnish founder diseases. (external link)

Academic article

• Labun, Kornel; Rio, Oline Eriksen; Tjeldnes, Håkon et al. (2025). CHOPOFF: symbolic alignments enable fast and sensitive CRISPR off-target detection. (external link)
• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Labun, Kornel et al. (2025). Precision T cell correction platform for Inborn Errors of Immunity. (external link)
• Tierney, Jack A.S.; Świrski, Michał I.; Tjeldnes, Håkon et al. (2025). RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. (external link)
• Sivertsen, Audun; Mortensen, Nicolay; Solem, Unni et al. (2024). Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected. (external link)
• Kelley, Leanne H.; Caldas, Ian V.; Sullenberger, Matthew T. et al. (2024). Poly(U) polymerase activity in Caenorhabditis elegans regulates abundance and tailing of sRNA and mRNA. (external link)
• Tierney, Jack A.S.; Sẃirski, Michał; Tjeldnes, Håkon et al. (2024). Ribosome decision graphs for the representation of eukaryotic RNA translation complexity. (external link)
• Svalastoga, Pernille; Kaci, Alba; Molnes, Janne et al. (2023). Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes. (external link)
• Bizuayehu, Teshome Tilahun; Labun, Kornel; Jakubec, Martin et al. (2022). Long-read single-molecule RNA structure sequencing using nanopore. (external link)
• Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle et al. (2022). Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. (external link)
• Tjeldnes, Håkon; Labun, Kornel; Cleuren, Yamila Nicole Torres et al. (2021). ORFik: a comprehensive R toolkit for the analysis of translation. (external link)
• Labun, Kornel; Krause, Maximilian; Cleuren, Yamila Nicole Torres et al. (2021). CRISPR Genome Editing Made Easy Through the CHOPCHOP Website. (external link)
• Chyzynska, Katarzyna; Labun, Kornel; Jones, Carl Matthew et al. (2021). Deep conservation of ribosome stall sites across RNA processing genes. (external link)
• Reint, Ganna; Li, Zhuokun; Labun, Kornel et al. (2021). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. (external link)
• Svalastoga, Pernille; Sulen, Åsta Nordsveen; Fehn, Jarle Røneid et al. (2020). Intellectual disability in KATP channel neonatal diabetes. (external link)
• Poduval, Deepak; Berge, Elisabet Ognedal; Sichmanovà, Zuzana et al. (2020). Assessment of tumor suppressor promoter methylation in healthy individuals. (external link)
• Giess, Adam; Cleuren, Yamila Nicole Torres; Tjeldnes, Håkon et al. (2020). Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. (external link)
• Pálfy, Máté; Schulze, Gunnar; Valen, Eivind et al. (2020). Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. (external link)
• Danks, Gemma Barbara; Galbiati, Heloisa; Raasholm, Martina et al. (2019). Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. (external link)
• Krause, Maximilian; Niazi, Adnan Muhammad; Labun, Kornel et al. (2019). tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. (external link)
• Labun, Kornel; Montague, Tessa G.; Krause, Maximilian et al. (2019). CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. (external link)
• Labun, Kornel; Guo, Xiaoge; Chavez, Alejandro et al. (2019). Accurate analysis of genuine CRISPR editing events with ampliCan. (external link)
• Birkeland, Åsmund; Chyzynska, Katarzyna; Valen, Eivind (2018). Shoelaces: An interactive tool for ribosome profiling processing and visualization. (external link)
• Giess, Adam; Jonckheere, Veronique; Ndah, Elvis et al. (2017). Ribosome signatures aid bacterial translation initiation site identification. (external link)
• Ndah, Elvis; Jonckheere, Veronique; Giess, Adam et al. (2017). REPARATION: ribosome profiling assisted (re-) annotation of bacterial genomes. (external link)
• Valen, Eivind; Labun, Kornel; Montague, Tessa G. et al. (2016). CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. (external link)
• Thyme, Summer B.; Akhmetova, Laila; Montague, Tessa G. et al. (2016). Internal guide RNA interactions interfere with Cas9-mediated cleavage. (external link)
• Merkle, Florian T.; Neuhausser, Werner M.; Santos, David et al. (2015). Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. (external link)
• Andersson, Robin; Andersen, Peter Refsing; Valen, Eivind et al. (2014). Nuclear stability and transcriptional directionality separate functionally distinct RNA species. (external link)

Masters thesis

• Holt, Eric; Halberg, Nils Henrik; Valen, Eivind (2024). The pancreas remembers: epigenetic memory of obesity as subtle, coordinated changes in promoter accessibility. (external link)

Lecture

• Reint, Ganna; Li, Zhuokun; Labun, Kornel et al. (2022). Rapid genome editing by CRISPR-Cas9-POLD3 fusion.. (external link)

Errata

• Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé et al. (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). (external link)

Academic literature review

• Kute, Preeti; Soukarieh, Omar; Tjeldnes, Håkon et al. (2022). Small Open Reading Frames, How to Find Them and Determine Their Function. (external link)
• Niazi, Adnan Muhammad; Krause, Maximilian; Valen, Eivind Dale (2021). Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA. (external link)

Editorial

• Valen, Eivind (2022). Nye CRISPR-metoder og mer presis presisjonsmedisin. (external link)

Doctoral dissertation

• Giess, Adam; Valen, Eivind (2019). Understanding translational landscapes through the footprints of ribosomes. (external link)

See a complete overview of publications in Cristin.

CRISPR genome engineering

RNA Biology

Nanopore sequencing

Regulation of Translation